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Ashraf S, Hikal WM, Almahallawi R, Muqaddas H, Iqbal F. Molecular prevalence, associated risk factors and phylogenetic evaluation of Theileria lestoquardi in the blood samples of small ruminants. PLoS One 2024; 19:e0306697. [PMID: 38990813 PMCID: PMC11238983 DOI: 10.1371/journal.pone.0306697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/23/2024] [Indexed: 07/13/2024] Open
Abstract
Raising small ruminants is the main source of income for farmers in Pakistan especially in rural areas of Dera Ghazi Khan in Punjab. Despite having large sheep population, the prevalence of intra-erythrocytic protozoa, Theileria (T.) lestoquardi, has never been reported from this area. This study was conducted to fill this knowledge gap and 333 blood samples of apparently healthy small ruminants (168 sheep and 165 goats) along with their epidemiological data were collected from Dera Ghazi Khan district during August till November 2022. The polymerase chain reaction (PCR) analysis amplified a 785 base pair amplicon specific for the Merozoite surface antigen (ms 1-2) gene of T. lestoquardi in 2 out of the 168 (3.3%) sheep blood samples, while no goat blood sample out of 165 was found to be infected with T. lestoquardi. DNA sequencing confirmed the presence of Theileria lestoquardi in both samples and phylogenetic analysis revealed that these amplicon resembled the partial ms 1-2 gene sequences detected in small ruminants from Pakistan, India Iran and Egypt. All the studied epidemiological factors (age, sex, breed, size of herd, dogs with herd, composition of herd, size of herd and Tick burden on sheep) were not found associated with the prevalence of T. lestoquardi. In conclusion, this study reports a low prevalence of T. lestoquardi infection in the Dera Ghazi Khan District of Punjab, Pakistan. The data generated from this work will help pave the way for the prophylactic detection and control of ovine and caprine theileriosis in the region.
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Affiliation(s)
- Sehrish Ashraf
- Department of Zoology, Emerson University Multan, Multan, Pakistan
- Department of Zoology, Ghazi University Dera Ghazi Khan, Ghazi Khan, Pakistan
| | - Wafaa M. Hikal
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Ruoa Almahallawi
- Department of Biology, University College of Duba, University of Tabuk, Tabuk, Saudi Arabia
| | - Hira Muqaddas
- Department of Zoology, The Women University Multan, Multan, Pakistan
| | - Furhan Iqbal
- Institute of Zoology, Bahauddin Zakariya University Multan, Multan, Pakistan
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Mishra AK, Ahlawat S, Sharma R, Arora R, Singh S, Jain A. Assessment of genetic diversity of the fat-tailed Dumba sheep of India by mitochondrial and microsatellite markers. Anim Biotechnol 2023; 34:3545-3554. [PMID: 36794377 DOI: 10.1080/10495398.2023.2176316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
India has a centuries-old tradition of sheep production and breeding that accomplish economic, agricultural, and religious roles. In addition to the 44 registered sheep breeds, there is a fat-tailed sheep population referred to as Dumba. This study evaluated genetic variation in Dumba sheep and its differentiation from other Indian sheep breeds using mitochondrial DNA and genomic microsatellite loci. Haplotype and nucleotide diversity based on mitochondrial DNA analysis revealed substantially high maternal genetic diversity in Dumba sheep. Major ovine haplogroups A and B observed in sheep populations across the globe registered their presence in the Dumba sheep. The molecular genetic analysis using microsatellite markers also showed high measures of allele (10.125 ± 0.762) and gene diversity (0.749 ± 0.029). Results correspond to the non-bottleneck population that is near mutation-drift equilibrium despite some deficiency in the number of heterozygotes (FIS = 0.043 ± 0.059). Phylogenetic clustering confirmed Dumba to be a distinct population. Results of this study endow authorities with critical information imperative for sustainable utilization and conservation of Indian fat-tailed sheep, which is considered to be an untapped genetic resource contributing to the food security, livelihood, and economic sustainability of rural households in marginal areas of the country.
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Affiliation(s)
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Sanjeev Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Anand Jain
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Hall SJG. Genetic Differentiation among Livestock Breeds-Values for F st. Animals (Basel) 2022; 12:1115. [PMID: 35565543 PMCID: PMC9103131 DOI: 10.3390/ani12091115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
(1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06-0.12, SNP 0.08-0.15; sheep: microsatellite 0.06-0.10, SNP 0.06-0.17; horses: microsatellite 0.04-0.11, SNP 0.08-0.12; goats: microsatellite 0.04-0.14, SNP 0.08-0.16; pigs: microsatellite 0.06-0.27, SNP 0.15-0.22; chickens: microsatellite 0.05-0.28, SNP 0.08-0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world's livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.
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Affiliation(s)
- Stephen J G Hall
- Department of Environmental Protection and Landscape, Estonian University of Life Sciences, Kreutzwaldi 5, 51014 Tartu, Estonia
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Sharma R, Ahlawat S, Sharma H, Sharma P, Panchal P, Arora R, Tantia MS. Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India. Sci Rep 2020; 10:20422. [PMID: 33235268 PMCID: PMC7687881 DOI: 10.1038/s41598-020-77480-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
Sheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (FST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.
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Affiliation(s)
- Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Himani Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Priyanka Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Poonam Panchal
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Wang SH, Zhang C, Shang M, Wu XG, Cheng YX. Genetic diversity and population structure of native mitten crab (Eriocheir sensu stricto) by microsatellite markers and mitochondrial COI gene sequence. Gene 2019; 693:101-113. [PMID: 30716435 DOI: 10.1016/j.gene.2018.12.083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/02/2018] [Accepted: 12/27/2018] [Indexed: 11/28/2022]
Abstract
Mitten crab (Eriocheir sensu stricto) is an indigenous and economically important species in East Asia. The genetic diversity and population structure of four wild native Eriocheir s. s. populations, from Yangtze (YZ), Oujiang (OJ), Minjiang (MJ), and Nanliujiang (NLJ) River basin, were studied. Genetic diversity of the four populations was evaluated by eight microsatellite and mitochondrial cytochrome oxidase subunits I (COI) markers. The polymorphism information content (PIC) values ranged from 0.7827 to 0.8580 and Shannon Wiener index (I) values varied from 2.0722 to 2.4088 respectively, according to microsatellite markers analysis. The haplotype diversity (h) values ranged from 0.52101 to 0.87097, while the values of nucleotide diversity (π) varied from 0.00139 to 0.02796 based on mitochondrial COI gene sequence. Four wild Eriocheir s. s. populations all showed high genetic diversity. As microsatellite analysis results, pair-wise FST values of YZ, OJ, MJ and NLJ populations were 0.1347, 0.1103 and 0.0943 respectively, which indicated that they were in medium genetic differentiation (0.05 < FST < 0.15). This was consistent with mitochondrial COI gene's conclusion. The bottleneck analysis was a hint that Eriocheir s. s. experienced bottleneck effect under SMM models of Sign Test and Wilcoxon Sign-rank Test. Based on genetic structure, YZ, OJ and MJ populations were in the same cluster separated from NLJ population. In summary, by microsatellite and mitochondrial COI markers analysis, all four Eriocheir s. s. populations had high genetic diversity, and genetic differentiation was consistent with geographical distance. Populations OJ and MJ were closer to population YZ genetically, and they had large genetic distance with NLJ population. This study provides a particularly important basis for mitten crab resources conservation and utilization in south China.
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Affiliation(s)
- Shi-Hui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Cheng Zhang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Fish Nutrition and Environmental Ecology Research Center, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Mei Shang
- Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Xu-Gan Wu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Fish Nutrition and Environmental Ecology Research Center, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Yong-Xu Cheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Fish Nutrition and Environmental Ecology Research Center, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
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